1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
#! /usr/bin/env python
from __future__ import print_function
import ruffus
import ruffus.drmaa_wrapper
import os
import sys
import time
try:
import drmaa
HAVE_DRMAA = True
DRMAA_SESSION = drmaa.Session()
DRMAA_SESSION.initialize()
except ImportError:
HAVE_DRMAA = False
logger, logger_mutex = ruffus.cmdline.setup_logging("me", "test.log", 1)
exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
sys.path.insert(0, os.path.abspath(os.path.join(exe_path, "..", "..")))
workdir = 'tmp_test_job_history_with_exceptions'
# sub-1s resolution in system?
one_second_per_job = None
throw_exception = False
def run_job(infile, outfile, **kwargs):
if not kwargs.get("run_locally", False):
kwargs["drmaa_session"] = DRMAA_SESSION
print("%s start to run " % infile)
stdout, stderr = ruffus.drmaa_wrapper.run_job(
cmd_str="sleep 100 && hostname > {}".format(os.path.abspath(outfile)),
verbose=1,
local_echo=False,
logger=logger,
**kwargs)
print("%s completed" % infile)
@ruffus.mkdir(workdir)
@ruffus.originate([workdir + "/" + prefix + "_name.tmp1" for prefix in "abcdefghijk"])
def generate_initial_files1(on):
with open(on, 'w') as outfile:
pass
@ruffus.transform(generate_initial_files1,
ruffus.suffix(".tmp1"), ".tmp2")
def test_task2(infile, outfile):
run_job(infile, outfile)
@ruffus.transform(test_task2, ruffus.suffix(".tmp2"), ".tmp3")
def test_task3(infile, outfile):
run_job(infile, outfile)
def cleanup_tmpdir():
os.system('rm -f %s %s' %
(os.path.join(workdir, '*'), ruffus.RUFFUS_HISTORY_FILE))
def do_main():
print("Press Ctrl-C Now!!", file=sys.stdout)
sys.stdout.flush()
time.sleep(2)
print("Start....", file=sys.stdout)
sys.stdout.flush()
ruffus.pipeline_run(verbose=5,
pool_manager="gevent",
multiprocess=5,
pipeline="main")
print("too late!!", file=sys.stdout)
sys.stdout.flush()
cleanup_tmpdir()
do_main()
|
